Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

[Larson Danes]

This all explains a lot. Thanks very much, Brian and Peter!

On Wed, Jan 18, 2017 at 6:05 PM, Peter S. Shenkin  wrote:

> In addition to Brian's observation, there is also a "C1" early in the
> SMILES, but no corresponding X1 to make a ring bond before or after it.
>
> It appears that you might be reading the second half of a SMILES for some
> reason. My guess is that the (C=C1) is associated with a preceding atom
> that was not read.
>
> -P
>
> On Wed, Jan 18, 2017 at 6:32 PM, Brian Kelley 
> wrote:
>
>> That doesn't look like a valid SMILES to me, I don't think a think a
>> smiles string can start with a parenthesis ( branch ).
>>
>> 
>> Brian Kelley
>>
>> On Jan 18, 2017, at 6:18 PM, Larson Danes  wrote:
>>
>> Hi all,
>>
>> I'm using the following query in postgresql (with the rdkit extension
>> installed):
>>
>> "select casrn from mols where m @> CAST(? AS mol)"
>>
>>
>> This returns "ERROR: could not create molecule from SMILES '...' " on 
>> occasion. One such SMILE that causes this error regularly is 
>> '(C=C1)[N+]([O-])=O'. I'm curious if there's documentation on this specific 
>> error message anywhere. I've looked and haven't had luck finding any.
>>
>> Any information about this error message is much appreciated.
>>
>>
>> Thanks,
>>
>>
>> Larson
>>
>> 
>> --
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>>
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>>
>
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Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

[Peter S. Shenkin]

In addition to Brian's observation, there is also a "C1" early in the
SMILES, but no corresponding X1 to make a ring bond before or after it.

It appears that you might be reading the second half of a SMILES for some
reason. My guess is that the (C=C1) is associated with a preceding atom
that was not read.

-P

On Wed, Jan 18, 2017 at 6:32 PM, Brian Kelley  wrote:

> That doesn't look like a valid SMILES to me, I don't think a think a
> smiles string can start with a parenthesis ( branch ).
>
> 
> Brian Kelley
>
> On Jan 18, 2017, at 6:18 PM, Larson Danes  wrote:
>
> Hi all,
>
> I'm using the following query in postgresql (with the rdkit extension
> installed):
>
> "select casrn from mols where m @> CAST(? AS mol)"
>
>
> This returns "ERROR: could not create molecule from SMILES '...' " on 
> occasion. One such SMILE that causes this error regularly is 
> '(C=C1)[N+]([O-])=O'. I'm curious if there's documentation on this specific 
> error message anywhere. I've looked and haven't had luck finding any.
>
> Any information about this error message is much appreciated.
>
>
> Thanks,
>
>
> Larson
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
> ___
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> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
> 
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> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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>
>
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Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

[Brian Kelley]

That doesn't look like a valid SMILES to me, I don't think a think a smiles 
string can start with a parenthesis ( branch ).


Brian Kelley

> On Jan 18, 2017, at 6:18 PM, Larson Danes  wrote:
> 
> Hi all,
> 
> I'm using the following query in postgresql (with the rdkit extension 
> installed):
> 
> "select casrn from mols where m @> CAST(? AS mol)"
> 
> This returns "ERROR: could not create molecule from SMILES '...' " on 
> occasion. One such SMILE that causes this error regularly is 
> '(C=C1)[N+]([O-])=O'. I'm curious if there's documentation on this specific 
> error message anywhere. I've looked and haven't had luck finding any.
> Any information about this error message is much appreciated.
> 
> Thanks,
> 
> Larson
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
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